Molecular Cell Biology

Research Output

Alternative states and population crashes in a resource-susceptible-infected model for planktonic parasites and hosts.

Gerla, D. J., Gsell, A., Kooi, B. W., Ibelings, W., van der Donk, E. & Mooij, W. M., 2013, In : Functional Ecology. 58, p. 538-551

Research output: Contribution to JournalArticleAcademicpeer-review

Altricial-precocial spectra in animal kingdom

Augustine, S., Lika, K. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 27-34 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A manipulative test of competing theories for metabolic scaling in animals.

White, C. R., Kearney, M. R., Matthews, P. G. D., Kooijman, S. A. L. M. & Marshall, D. J., 2011, In : The American Naturalist. 178, p. 746-754

Research output: Contribution to JournalArticleAcademicpeer-review

A mathematical model for yeast respiro-fermentative physiology.

Hanegraaf, P. P. F., Stouthamer, A. H. & Kooijman, S. A. L. M., 2000, In : Yeast. 16, p. 423-437

Research output: Contribution to JournalArticleAcademicpeer-review

A mathematical modeling approach to assessing the reliabilty of biomarkers of glutathione metabolism.

Geenen, S., du Preez, F. B., Reed, M., Nijhout, H. F., Kenna, J. G., Wilson, I. D., Westerhoff, H. V. & Snoep, J. L., 16 Jul 2012, In : European Journal of Pharmaceutical Sciences. 46, 4, p. 233-243 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A mathematical model that accounts for the effects of caloric restriction on body weight and longevity.

van Leeuwen, I. M. M., Kelpin, F. L. D. & Kooijman, S. A. L. M., 2002, In : Biogerontology. 3, p. 373-381

Research output: Contribution to JournalArticleAcademicpeer-review

A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage

Puniya, B. L., Todd, R. G., Mohammed, A., Brown, D. M., Barberis, M. & Helikar, T., 2 Aug 2018, In : Frontiers in Physiology. 9, AUGUST, p. 1-18 18 p., 878.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Ameliorating effects of industrial sugar residue on the Jales gold mine spoil NE Portugal) using Holcus lanatus and Phaseolus vulgaris as indicators.

Bleeker, P. M., Teiga-Santos, M. H., de Koe, T. & Verkley, J. A. C., 2003, In : Environmental Pollution. 125, p. 237-244

Research output: Contribution to JournalArticleAcademicpeer-review

A metabolic control analysis of kinetic controls in ATP free energy metabolism in contracting skeletal muscle.

Jeneson, J. A. L., Westerhoff, H. V. & Kushmerick, M. J., 2000, In : American Journal of Physiology. 279, p. C813-C832

Research output: Contribution to JournalArticleAcademicpeer-review

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Damiani, C., Colombo, R., Gaglio, D., Mastroianni, F., Pescini, D., Westerhoff, H. V., Mauri, G., Vanoni, M. & Alberghina, L., 1 Sep 2017, In : PLoS Computational Biology. 13, 9, e1005758.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A method for introduction of unmarked mutations in the genome of Paracoccus denitrificans: construction of strains with multiple mutations in the genes encoding periplasmic cytochromes c550, c551i, and c553i

Van Spanning, R. J., Wansell, C. W., Reijnders, W. N., Harms, N., van Ras, N. J. P., Oltmann, L. F. & Stouthamer, A. H., Nov 1991, In : Journal of Bacteriology. 173, 21, p. 6962-70 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A method for studying plasma membrane transport with intact cells using computerized fluorometry.

Wielinga, P. W., Heijn, M., Westerhoff, H. V. & Lankelma, J., 1998, In : Analytical Biochemistry. 263, p. 221-231 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A Million-Fold Speed Improvement in Genomic Repeats Detection.

Romein, J. W., Heringa, J. & Bal, H. E., 2003, SC. ACM, p. 20

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Amino acid analysis using chromatography–mass spectrometry: An inter platform comparison study

Krumpochova, P., Bruyneel, B., Molenaar, D., Koukou, A., Wuhrer, M., Niessen, W. M. A. & Giera, M. A., 2015, In : Journal of Pharmaceutical and Biomedical Analysis. 114, p. 398-407

Research output: Contribution to JournalArticleAcademicpeer-review

A mixed-species microarray for identification of food spoilage bacilli

Caspers, M. P. M., Schuren, F. H. J., van Zuijlen, A. C. M., Brul, S., Montijn, R. C., Abee, T. & Kort, R., Apr 2011, In : Food microbiology. 28, 2, p. 245-51 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., Pir, P., Simeonidis, E., Spasic, I., Wishart, J., Weichart, D., Hayes, N. W., Jameson, D., Broomhead, D. S., Oliver, S. G., Gaskell, S. J. & 5 others, McCarthy, J. E. G., Paton, N. W., Westerhoff, H. V., Kell, D. B. & Mendes, P., 2013, In : The FEBS Journal. 587, p. 2832-2841

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A model to analyze effects of comlex mixtures on survival.

Baas, J., Jager, T. & Kooijman, S. A. L. M., 2009, In : Ecotoxicology and Environmental Safety. 72, p. 669-676

Research output: Contribution to JournalArticleAcademicpeer-review

A modular kinetic approach to determine which step in electron transfer from external NAD(P)H to oxygen in potato callus mitochondria is stimulated by high salt conditions

Krab, K., Wagner, A. M., Wagner, M. J. & Moller, I. M., 1998, Plant Mitochondria: From gene to function. Moller, I. M., Gardestrom, P., Glimenius, K. & Glaser, E. (eds.). Leiden - The Netherlands: Backhuys Publishers, p. 537-541 603 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

A molecular movie at 1.8 A resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds

Ren, Z., Perman, B., Srajer, V., Teng, T. Y., Pradervand, C., Bourgeois, D., Schotte, F., Ursby, T., Kort, R., Wulff, M. & Moffat, K., 20 Nov 2001, In : Biochemistry. 40, 46, p. 13788-801 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells

van Tatenhove-Pel, R. J., Zwering, E., Solopova, A., Kuipers, O. P. & Bachmann, H., 1 Dec 2019, In : Scientific Reports. 9, 1, 9867.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Ample arsenite bio-oxidation activity in Bangladesh drinking water wells: A bonanza for bioremediation?

Hassan, Z., Sultana, M., Khan, S. I., Braster, M., Röling, W. F. M. & Westerhoff, H. V., Aug 2019, In : Microorganisms. 7, 8, p. 1-22 22 p., 246.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores.

de Boer, P., Caspers, M., Sanders, J. W., Kemperman, R., Wijman, J., Lommerse, G., Roeselers, G., Montijn, R., Abee, T. & Kort, R., 2015, In : Microbiome. 27, p. 30 3.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4+/NH3

Boogerd, F. C., Ma, H., Bruggeman, F. J., van Heeswijk, W. C., Garcia-Contreras, R., Molenaar, D., Krab, K. & Westerhoff, H. V., 3 Jan 2011, In : FEBS Letters. 585, 1, p. 23-28

Research output: Contribution to JournalArticleAcademicpeer-review

A multielement analysis of C u induced changes in the mineral profiles of Cu sensitive and Cu tolerant populations of Silene paradoxa L.

Pignatelli, S., Colzi, I., Buccianti, A., Cattani, I., Beone, G. M., Schat, H. & Gonnelli, C., 2013, In : Environmental and Experimental Botany. 90, p. 20-27

Research output: Contribution to JournalArticleAcademicpeer-review

A multivariate geostatistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles.

Mouser, P. J., Rizzo, D. M., Roling, W. F. M. & van Breukelen, B. M., 2005, In : Environmental Science and Technology. 39, p. 7551-7559 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A Mutant of Paracoccus denitrificans with Disrupted Genes Coding for Cytochrome c 550 and Pseudoazurin Establishes These Two Proteins as the In Vivo Electron Donors to Cytochrome cd 1 Nitrite Reductase

Pearson, I. V., Page, M. D., Van Spanning, R. J. M. & Ferguson, S. J., 1 Nov 2003, In : Journal of Bacteriology. 185, 21, p. 6308-6315 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Anaerobic biodegradation of crude oil under sulphate-reducing conditions leads to only modest enrichment of recognized sulphate-reducing taxa

Sherry, A., Gray, N. D., Ditchfield, A. K., Aitken, C. M., Jones, D. M., Roling, W. F. M., Hallmann, C., Larter, S. R., Bowler, B. F. J. & Head, I. M., 2013, In : International Biodeterioration & Biodegradation. 81, p. 105-113

Research output: Contribution to JournalArticleAcademicpeer-review

Anaerobic growth of Paracoccus denitrificans requires cobalamin: characterization of cobK and cobJ genes

Shearer, N., Hinsley, A. P., Van Spanning, R. J. & Spiro, S., Nov 1999, In : Journal of Bacteriology. 181, 22, p. 6907-13 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence

Sturme, MHJ., Nakayama, J., Molenaar, D., Murakami, Y., Kunugi, R., Fujii, T., Vaughan, E. E., Kleerebezem, M. & Vos, W. M., Aug 2005, In : Journal of Bacteriology. 187, 15, p. 5224-5235

Research output: Contribution to JournalArticleAcademicpeer-review

An alternative model for haem ligation in nitrate reductase and analogues respiratory cytochrome b complexes.

van der Oost, J., Nederkoorn, P. H. J., Stouthamer, A. H., Westerhoff, H. V. & van Spanning, R. J. M., 1996, In : Molecular Microbiology. 22, 1, p. 193-196

Research output: Contribution to JournalArticleAcademicpeer-review

An alternative P-II protein in the regulation of glutamine synthetase in Escherichia coli

vanHeeswijk, WC., Hoving, S., Molenaar, D., Stegeman, B., Kahn, D. & Westerhoff, HV., Jul 1996, In : Molecular Microbiology. 21, 1, p. 133-146

Research output: Contribution to JournalArticleAcademicpeer-review

Analyses of four centuries of bounty hunting on seals in Zeeland, sw-netherlands.

de Vooys, K. G. N., Brasseur, S. M. J. M., van der Meer, J. & Reijnders, P. J. H., 2012, In : Lutra. 55, p. 55-65

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of an asymmetric two-strain dengue model.

Kooi, B. W., Aguiar, M. & Stollenwerk, N., 2014, In : Mathematical Biosciences. 248, p. 128-139

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of a predator–prey model with specific time scales:a geometrical approach proving the occurrence of canard solutions

Poggiale, J. C., Aldebert, C., Girardot, B. & Kooi, B. W., 2020, In : Journal of Mathematical Biology. 80, 1-2, p. 39-60 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of Arabidopsis thaliana HKT1 and Eutrema salsugineum/botschantzevii HKT1;2 Promoters in Response to Salt Stress in Athkt1:1 Mutant

Nawaz, I., Iqbal, M., Hakvoort, H. W. J., de Boer, A. H. & Schat, H., 1 Jun 2019, In : Molecular Biotechnology. 61, 6, p. 442-450 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Analysis of arsenic in soil and vegetation of a contaminated area in Zarshuran, Iran

Karimi, N., Ghaderian, S. M., Maroofi, H. & Schat, H., 2010, In : International Journal of Phytoremediation. 12, 2, p. 159-173 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of bHLH and MYB-domain proteins: species-specific regulatory differences caused by divergent evolution of target anthocyanin genes

Quattrocchio, F. M., Wing, J. F., van der Woude, J. F., Mol, J. N. M. & Koes, R. E., 1998, In : Plant Journal. 13, p. 475-488 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of bioassays with time-varying concentrations.

Pery, A. R. R., Bedaux, J. J. M., Zonneveld, C. & Kooijman, S. A. L. M., 2001, In : Water Research. 35, p. 3825-3832

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of concentration response curves to describe and compare tha antimicrobial activity anof model cationic alpha-helical peptides.

Rautenbach, M., Gerstner, G. D., Vlok, N. M., Kulenkampff, J. & Westerhoff, H. V., 2006, In : Analytical Biochemistry. 350, p. 81-90 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of effects of 2,2',5,5'-tetracholorobiphenyl on the flux control in oxidative phosphorylation system in rat liver mitochondria.

Mildaziene, V., Nauciene, Z., Baniene, R., Demin, O. V. & Krab, K., 2002, In : Molecular Biology Reports. 29, p. 35-40

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of flower pigmentation mutants generated by random transposon mutagenesis

van Houwelingen, A., Souer, E. J., Spelt, C. E., Beusekom-Kloos, R., Mol, J. N. M. & Koes, R. E., 1998, In : Plant Journal. 13, p. 39-50 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

Teusink, B., Wiersma, A., Molenaar, D., Francke, C., de Vos, W. M., Siezen, R. J. & Smid, E. J., 29 Dec 2006, In : Journal of Biological Chemistry. 281, 52, p. 40041-40048

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of microbial communities in a landfill leachate polluted aquifer using a new method for anaerobic physiological profiling and 16S rDNA Fingerprinting.

Roling, W. F. M., van Breukelen, B. M., Braster, M., Goeltom, M. T., Groen, J. & van Verseveld, H. W., 2000, In : Microbial Ecology. 40, p. 177-188

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of multiple gene expression array experiments after repetitive hybridisations on nylon membranes.

Hornberg, J. J., de Haas, R. R., Dekker, H. & Lankelma, J., 2002, In : BioTechniques. 33, p. 108-117 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector.

van der Woude, A. D., Stoop, E. J. M., Stiess, M., Wang, Q., Ummels, R., van Stempvoort, G., Piersma, S. R., Cascioferro, A., Jimenez, C. R., Houben, E. N. G., Luirink, J., Pieters, J., van der Sar, A. M. & Bitter, W., 2014, In : Cellular Microbiology. 16, 2, p. 280-295

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of single quantum-dot mobility inside 1D nanochannel devices

Hoang, T. H., Segers-Nolten, I. M. J., Tas, N. R., van Honschoten, J. W., Subramaniam, V. & Elwenspoek, M. C., 8 Jul 2011, In : Nanotechnology. 22, 27, p. 275201

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach

Hettling, H., Heringa, J. & van Beek, J. H. G. M., 2010, In : BMC Bioinformatics. 11, Suppl. 10, p. O9

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Analysis of the hierarchical and metabolic regulation of flux through metabolic pathways.

Roling, W. F. M., Fillinger, L. & Nunes da Rocha, U., 2014, (Accepted/In press) Hydrocarbon and lipid microbiology protocols.. Timmis, K. N. (ed.). Berlin-Heidelberg: Springer Verlag

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Analysis of the regulation of the rate of hydrocarbon and nutrient flow through microbial communities.

Roling, W. F. M., Fillinger, L. & Nunes da Rocha, U., 2014, Hydrocarbon and Lipid Microbiology Protocols.. Timmis, K.N. (ed.). Humana Press

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review